Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

This page was generated on 2023-03-29 11:06:17 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4301
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for HiCBricks on merida1


To the developers/maintainers of the HiCBricks package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCBricks.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 911/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.17.0  (landing page)
Koustav Pal
Snapshot Date: 2023-03-28 14:00:22 -0400 (Tue, 28 Mar 2023)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: d85dbc7
git_last_commit_date: 2022-11-01 11:18:41 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCBricks
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.17.0.tar.gz
StartedAt: 2023-03-29 01:16:33 -0400 (Wed, 29 Mar 2023)
EndedAt: 2023-03-29 01:23:29 -0400 (Wed, 29 Mar 2023)
EllapsedTime: 415.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiCBricks’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
Brick_export_to_sparse           5.490  0.239   7.898
Brick_vizart_plot_heatmap        4.412  0.205   6.048
BrickContainer_unlink_resolution 3.957  0.144   5.619
Brick_local_score_differentiator 3.760  0.218   5.090
Brick_add_ranges                 3.874  0.084   5.301
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

HiCBricks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘HiCBricks’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HiCBricks)

Tests output


Example timings

HiCBricks.Rcheck/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name2.6230.1103.769
BrickContainer_change_output_directory1.9630.0712.712
BrickContainer_get_path_to_file1.8150.0622.449
BrickContainer_list_chromosomes1.8090.0612.459
BrickContainer_list_experiment_name1.8250.0602.494
BrickContainer_list_files1.8410.0612.508
BrickContainer_list_output_directory1.8370.0622.471
BrickContainer_list_resolutions1.8040.0622.412
BrickContainer_unlink_resolution3.9570.1445.619
Brick_add_ranges3.8740.0845.301
Brick_call_compartments2.8340.1794.165
Brick_export_to_sparse5.4900.2397.898
Brick_fetch_range_index2.1460.0643.089
Brick_fetch_row_vector3.5260.1514.882
Brick_get_bintable1.8220.0582.545
Brick_get_chrominfo1.7510.0582.391
Brick_get_entire_matrix2.5440.1613.607
Brick_get_matrix2.4600.1373.402
Brick_get_matrix_mcols2.4580.1473.395
Brick_get_matrix_within_coords3.5050.1524.818
Brick_get_ranges1.9020.0602.684
Brick_get_values_by_distance2.7410.1753.697
Brick_get_vector_values2.5250.1393.454
Brick_list_matrices1.7970.0592.554
Brick_list_matrix_mcols1.7400.0582.396
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys1.7530.0572.373
Brick_list_ranges_mcols1.7420.0612.352
Brick_load_cis_matrix_till_distance2.2930.1173.151
Brick_load_data_from_mcool0.0000.0010.000
Brick_load_data_from_sparse000
Brick_load_matrix2.4040.1393.331
Brick_local_score_differentiator3.7600.2185.090
Brick_make_ranges0.0200.0010.027
Brick_matrix_dimensions2.4080.1363.429
Brick_matrix_exists2.3930.1453.320
Brick_matrix_filename2.4050.1333.291
Brick_matrix_isdone2.4290.1393.304
Brick_matrix_issparse2.4370.1393.308
Brick_matrix_maxdist2.4350.1293.261
Brick_matrix_minmax2.4150.1293.272
Brick_mcool_normalisation_exists0.0010.0000.000
Brick_rangekey_exists1.7710.0622.334
Brick_return_region_position1.9760.0612.552
Brick_vizart_plot_heatmap4.4120.2056.048
Create_many_Bricks1.8050.0692.428
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer1.8880.0632.552